Gene-ius: ‘AquaLeap’ selective breeding project

In January of this year, a 3-year project on selective breeding called ‘AquaLeap’ was initiated, as part of the BBSRC and NERC UK Aquaculture Initiative. The project focuses entirely on genetics and breeding, specifically within the UK sector. The researchers behind the study are from the University of Stirling and over the next 3 years will be examining ways to advance aquaculture production through genetics and breeding.

Innovation in Aquaculture Genetics

Sustainable and profitable aquaculture in the UK relies on high quality stock. In contrast to terrestrial agriculture, the sources of stock for aquaculture species range from use of wild stock for several species, to pedigree-based breeding programmes incorporating genomic tools in salmon.

The investigation team highlight the need for, ‘well managed programmes of domestication and breeding have huge potential for cumulative gains in production, including the prevention of infectious disease outbreaks’. They add that, ‘barriers to applying such approaches in commercial aquaculture include knowledge gaps in the genetic basis of economically important traits, and a lack of genetic tools and expertise applied to aquaculture’.

‘AquaLeap’ establishes a leading interdisciplinary hub focused on innovation in aquaculture genetics to enable each sector to take a ‘step’ or ‘leap’ forward in stock enhancement.

Domestication and Breeding Programmes

Advances for four species will be targeted relating to their economic importance or potential for UK aquaculture; European lobster (Homarus gammarus), European flat oyster (Ostrea edulis), lumpfish (Cyclopterus lumpus) and Atlantic salmon (Salmo salar). For each of these species, genomic tools and methods will be developed, which will then be used to tackle industry-defined barriers to progress in stock enhancement.

Genomic tools will be implemented to support domestication and breeding programmes for all theses species. This will include high quality reference genome sequences using cutting-edge sequencing technology for the species for which they are currently lacking (lobster, oyster, lumpfish). These genome sequences will be used to exploit standard (e.g. single nucleotide polymorphism, SNP) and novel [e.g. copy number variation (CNV) and epigenetic modifications] sources of variation. Gene editing techniques will be developed, as this technology is likely to lead to breakthroughs in addressing aquaculture problems in the near future.

Lobsters are a high value species with potential for diversifying UK aquaculture. Building on previous studies into the on-growing of hatchery-reared lobsters in aquaculture systems, and using the aforementioned genomic tools, the team will assess the contribution of genetic and epigenetic variation to growth and survival traits. These results will inform selective breeding, hatchery conditions and choice of juveniles for on-growing, and has potential to improve the performance of lobsters at sea.

Native oysters have declined dramatically in recent years, and there is significant interest in restocking from both an aquaculture and ecological perspective. A major barrier to hatchery-based restocking and production is the parasitic disease Bonamia. By building on previous genomic tool development to identify SNP markers that can be used to predict breeding animals with innate resistance to Bonamia, informing selection of native oysters for stocking and tackling a major production issue. Pacific Oysters (Crassostrea gigas) have also been under examination, as they are the only species of shellfish susceptible to the oyster herpes virus.

Lumpfish are used extensively as cleaner fish for biological control of sea lice in salmon farming. Hatchery reproduction is now possible, and the next step is selective breeding for traits to enhance their robustness and performance. To help facilitate this, we will assess wild stock diversity to inform base populations for breeding, to estimate genetic parameters for production traits, and develop SNP marker panels for stock management.

Breeding of salmon is advanced, and uses genomic tools to enhance trait improvement and inbreeding control via genomic selection (GS). We will apply innovative approaches to improve the cost-efficiency of GS, and test these approaches for the emerging aquaculture species. We will assess the role of potential novel sources of genetic variation (CNVs) in gill health traits. Finally, we will use gene editing to modify a specific gene causing resistance to a viral disease in salmon, with a view to future editing of salmon genes to improve resistance to infectious diseases.

Salmon has tended to lead the way in genetic technology, due to demand and financial growth in the sector, so many companies have their own specialized breeding programmes, such as; Benchmark, Hendrix, AquaGen and Mowi.

Project Partners Represent Diversity of Sector

The scientific programme is complemented by a series of training, dissemination and public engagement activities, including addressing skills gaps identified by the ARCH-UK network.

Project partners include Hendrix, Otter Ferry Sea Fish, Xelect, Tethys Oysters and the National Lobster Hatchery, these companies represent the diversity of sectors and species.

The primary goal of AquaLeap is to tackle industry-defined barriers to advances in selective breeding and domestication of aquaculture species.

Genomic Tools and Technique Development

The development of appropriate underpinning genomic tools and techniques will be implemented, and then applied to specific end-user-defined problems in three ’emerging’ species (European lobster, European flat oyster, Lumpfish) and one ‘established’ species (Atlantic salmon.)

The reference genome assemblies for the emerging species will be created using 10X genomics and PacBio sequencing approaches. These will underpin several downstream tasks, including choice of SNP marker panels for stock management and breeding value calculations, genotype imputation and study of epigenetic marks using bisulphite sequencing.

Overview

In lobster, mixed model approaches will be used to estimate heritability for growth and survival traits, they will also assess the relative contribution of genetics and epigenetics to these traits.
In oyster, a recently developed SNP array to study resistance to Bonamia will be used, harnessing data from a large-scale laboratory disease challenge.
In lumpfish, stock diversity will be assessed using RAD-Sequencing to inform choice of animals for base populations, and heritability of production traits will also be assessed.
In salmon, the contribution of copy number variants to genetic variation in disease resistance will be assessed, with a focus on gill health traits.

Across all species, we will develop SNP marker panels for parentage and stock management, and also use the genomic resources to test imputation approaches to improve the affordability of genomic selection via combined parentage – imputation panels.

Gene editing has transformative potential for aquaculture and we will improve CRISPR-Cas9 editing techniques in salmon, and use editing to target putative causative variants underlying a major disease resistance QTL in salmon cell lines and embryos.

Planned Impact

AquaLeap is based on close cooperation and interdependency between the academic and non-academic partners, providing clear routes for immediate translation of research results. The following groups can expect positive impact from the proposal:

(i) UK and global aquaculture production: The immediate impacts will be via project partners. The focus on several emerging species will also assist with UK aquaculture diversification, which is an important component of maximising sustainable production and minimising risk.

(ii) Genetic services industry: There are several companies in the UK and globally whose core business is to support aquaculture breeding and production by offering genetic services, including management of breeding programmes.

(iii) UK economy: This project has potential for long term impact for the UK economy via improved sustainable production of various high quality food products with reduced environmental impact. There will be direct contribution to the UK treasury via improved competitiveness and market share for project partners, and also downstream positive impacts on fish farming companies, and the communities that depend on these industries.

(iv) UK science capacity. This project will enable capacity and expertise for use of genetic and genomic tools to answer fundamental biological questions via research programmes in academia and industry. This includes the development of universal genomic resources such as reference genome assemblies and SNP panels. This should help cement the position of the UK as a leading country in aquaculture bioscience.

(v) Political and regulatory bodies. Aquaculture is assuming increasing political importance, and solutions to production and environmental issues are key to its expansion. The outputs of this project may influence ethical and regulatory frameworks to encourage exploitation of new breeding technologies such as gene editing.

(vi) General public and society. This project has potential to influence societal attitudes to aquaculture, including use of selective breeding and gene editing. In the longer term, there will be direct benefits to society via improved economic stability and reduced environmental impact of the aquaculture industry.

Principal Investigator Andrew Davie shares the news about the project on Twitter saying, “New year and a new project to start… @Aqua_Leap is going to deliver significant techincal advances to the UK aquaculture sector!”

Biotechnology and Biological Sciences Research Council

Andrew Davie (Principal Investigator)
John Bernard Taggart (Co-Investigator)
Michaël Bekaert (Co-Investigator)
Herve Migaud (Co-Investigator)
Sarah-Louise Counter Selly (Researcher Co-Investigator)

Editor: AquacultureList


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